It didn’t attract much notice at the time, but one of the first moves of the new president of Harvard University, Drew Gilpin Faust, was to write to the chief of the union of British academics that was proposing a boycott of Israeli professors and universities. According to a statement from Ms. Faust’s office, she wrote the letter on her second day on the job at Harvard, expressing her own “conviction that such a move subverts the academic values and freedoms necessary to the free flow of ideas that are the lifeblood of universities and, ultimately, that of the societies and world we serve.”

Ms. Faust’s statement said that she joins “many colleagues throughout the international academic community in denouncing unequivocally an action that would serve no purpose and would fundamentally violate the academic freedoms we must defend at all costs.” It was a milder statement than the one from the president of Columbia, Lee Bollinger, who called the proposed boycott an “intellectually shoddy and politically biased” attempt “to hijack the central mission of higher education.” But it nonetheless made clear where Ms. Faust stood in respect of fair treatment of Israel.

The stance taken by Ms. Faust on the matter is closely watched, and is particularly welcome, because there was more than a whiff of anti-Israel — even anti-Jewish, some students sense — sentiment in the faculty rebellion that forced Ms. Faust’s predecessor, Lawrence Summers, from Massachusetts Hall. The Faculty of Arts and Sciences motion in March 2005 expressing no confidence in Mr. Summers was made by a Harvard professor, J. Lorand Matory, who had signed a petition calling on Harvard to divest from Israel.

That petition, like the British boycott effort, singled out Israel for opprobrium among all the countries of the world, and Mr. Summers, showed the courage to reject it, more bluntly than other university presidents, as being anti-Semitic in effect, if not intent. That position earned Mr. Summers the enmity not only of Mr. Matory but no doubt others on the faculty who are hostile to Israel. With Mr. Summers gone, there is no doubt that the anti-Israel camp at Harvard will try to gain ground.

Mr. Matory himself surfaced last week with an opinion piece in the student newspaper, the Crimson, with a new sneer at Zionism. “The convention that persecuted Europeans had the right to safe havens on lands stolen from non-Europeans was, by the mid-20th century, as outmoded as the Confederacy’s defense of slavery in the mid-19th,” he wrote. A professor at the Kennedy School of Government, Stephen Walt, has joined with a former colleague at the University of Chicago, John Mearsheimer, in writing a book that blames Israel and its American supporters for inspiring everything from the Iraq War to Al Qaeda terrorism against America.

Israel has its defenders on Harvard’s campus, including, among others, Alan Dershowitz at the Law School, Ruth Wisse, the Peretz professor of Yiddish literature, and an active group of Jewish students. But there is a sense after the ouster of Mr. Summers and the animus of Messrs. Matory and Walt that things are in the balance. There is room within any large institution for divergent points of view, even on questions as basic as the existence of Israel, but there is also room for a dominant point of view — which throws into sharp relief Harvard’s responsibilities as an American university in wartime.

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Harvard rose to the occasion in World War II. It may have been slow to support the war before it began, but once it did, Harvard’s president, James Bryant Conant, turned the campus over to training troops and the development of radar countermeasures. Conant himself served as chairman of the National Defense Research Committee and helped to develop the atom bomb that beat the Japanese. In the Cold War, while Harvard students eventually fell away from the fight for Vietnam, the cause of anti-communism was, at least for years, championed by such Harvard men as McGeorge Bundy, who left his post as dean of Harvard’s Faculty of Arts and Sciences to serve as national security adviser to that great cold warrior, President Kennedy, and Henry Kissinger, who went on to win the Nobel Prize for Peace.

With the outbreak of a new world war on September 11, 2001, Mr. Summers tried to rally Harvard to the American cause, going so far as to begin attending ROTC commissioning ceremonies. He had, after all, served as Treasury Secretary, the officer to which presidents often turned to raise an army. The reserve officers training corps had been thrown off the Harvard campus after Vietnam, and kept off ostensibly in response to the ban on gays in the military. Ms. Faust took office in July, but her formal installation is scheduled for October 12 in a ceremony with traditions dating back to Harvard’s founding in the 17th-century. One of the things people will be watching for her to say at that moment will be some words about the responsibilities of a university to its country in a war against an enemy determined not only to destroy Israel but also the rest of Western civilization.